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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagtttttgcataaggttatctcgcagtggaggatgtctctgtaggtcatatcgaggacgtaatttgtcccaactgtagttgcacatctatcttttga...

Basic information

species Physcomitrella patens
transcript PP1S29_256V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S29_256V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagtttttgcataaggttatctcgcag--tggaggatgtctctgtaggtcatatcgaggacgtaatt-tgtcccaactgtagttgcacatctatcttttga
 ||||||||||| ||||| |||||||| |||||||| |||||||||||||| || |||||    | ||   | | ||| |   |  | ||||| || ||  |   | ||   | |  || | |||    |   |||                   
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagttt----acaattctgtttcgtaaactcaaagatgtatcggttagaagtctcttagtccaaactgtgttttcaacatag-------------------
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|37845830|gb|BJ603838.1|BJ603838
EST:     TTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: TTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162169757|gb|FC345294.1|FC345294
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|37845305|gb|BJ603313.1|BJ603313
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|18327390|gb|BJ159392.1|BJ159392
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162182768|gb|FC359515.1|FC359515
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|67720249|gb|BJ970508.1|BJ970508
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|67727192|gb|BJ977451.1|BJ977451
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162176348|gb|FC353533.1|FC353533
EST:     TCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: TCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|18334218|gb|BJ166234.1|BJ166234
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|67726751|gb|BJ977010.1|BJ977010
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162171617|gb|FC347558.1|FC347558
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162181163|gb|FC357608.1|FC357608
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|37824766|gb|BJ582832.1|BJ582832
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|18335658|gb|BJ167678.1|BJ167678
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|67727852|gb|BJ978111.1|BJ978111
EST:     ATGGTGGAGGAATGAGCTCTGTCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162223700|gb|FC399772.1|FC399772
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|19789330|gb|BQ041244.1|BQ041244
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162176594|gb|FC353063.1|FC353063
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162223699|gb|FC399771.1|FC399771
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162182767|gb|FC359514.1|FC359514
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162167231|gb|FC342796.1|FC342796
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|18333553|gb|BJ165568.1|BJ165568
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|67725967|gb|BJ976226.1|BJ976226
EST:     ATGGTGGAGGAATGAGCCCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|67720690|gb|BJ970949.1|BJ970949
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|208375034|gb|DC944815.1|DC944815
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|67720235|gb|BJ970494.1|BJ970494
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT
EST: gi|162241271|gb|FC416902.1|FC416902
EST:     ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGT                         GTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGGTAACACCATT
genomic: ATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 35 (downstream exon)
Score: 16

ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagttttt ... tccttatcagGTGCTTGCATTCGAGGCTGGCAGGAAGTATGGCATTCGGGTTAACACCATTTCAGCAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGGTGGAGGAATGAGCTCTGCCAAGGCTGCACTTGAGAGTGACACACGTgtaagtttttgcataaggttatctcgcagtggaggatgtctctgtaggtcatatcgaggacgtaatttgtcccaactgtagttgcacatctatcttttga

-  TGGTGG
- - GGTGGA
- -  GTGGAG
- - - TGGAGG
- - -  GGAGGA